SMTL ID : 7sbv.1

Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

15 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.137, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: R.147, I.149, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.137, Q.169, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: N.342, E.346, N.371, S.374, F.378, T.616, Q.619 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.378 NAG-NAG.7: 5 residues within 4Å: Chain B: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.137, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain C: N.342, N.344, E.346, N.371, S.374, T.616, Q.619 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.713 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: F.726, D.727, N.738, T.740 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: R.147, L.162, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: H.693, N.695, Y.759 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.9: 6 residues within 4Å: Chain B: R.147, I.149, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP)

23 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.17: 2 residues within 4Å: Chain A: D.210, N.212 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain A: N.342, E.346, N.371, S.374, T.616, Q.619 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: A.448, N.449 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.713 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.787 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: A.932, N.935, N.936, G.940 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: S.654, I.673, T.674, N.675 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.695, Y.759, S.760 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: E.646, V.647, N.648 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.212 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.449 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.713 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: S.785, N.787 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.932, A.933, N.936 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: S.654, I.673, T.674, N.675 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.695, Y.759, S.760 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: E.646, V.647, N.648 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: L.159, N.212 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: A.448, N.449 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.787 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: A.932, A.933, N.936, G.940 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: S.654, I.673, N.675 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: E.646, V.647, N.648 Ligand excluded by PLIP

3 x 8Z9: Sapienic acid(Non-covalent)

8Z9.34: 17 residues within 4Å: Chain A: F.370, M.372, L.375, M.376, I.379, A.381, F.384, A.391, I.394, Y.395, I.402, L.441, L.603, L.605 Chain B: N.421, L.422, G.423 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:N.421, A:F.370, A:L.375, A:I.379, A:A.381, A:F.384, A:I.402, A:L.441, A:L.441, A:L.605 Hydrogen bonds: B:L.422, B:G.423, A:Y.395 8Z9.35: 16 residues within 4Å: Chain B: F.370, M.372, L.375, M.376, I.379, F.384, A.391, I.394, Y.395, I.402, L.603, L.605 Chain C: D.416, N.421, L.422, G.423 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.370, B:L.375, B:I.379, B:F.384, B:I.394, B:I.402, B:L.603, B:L.605 Hydrogen bonds: C:N.421, C:L.422 8Z9.42: 17 residues within 4Å: Chain A: V.415, D.416, N.421, L.422, G.423 Chain C: F.370, M.372, L.375, M.376, I.379, F.384, A.391, I.394, Y.395, I.402, L.603, L.605 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:V.415, C:F.370, C:L.375, C:I.379, C:F.384, C:I.394, C:I.402, C:L.605 Hydrogen bonds: A:L.422, C:Y.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bangaru, S. et al., Structural mapping of antibody landscapes to human betacoronavirus spike proteins. Sci Adv (2022)

Release Date

2022-05-04

Peptides

Spike protein: ABC
Human polyclonal Fab model with polyalanine backbone - Heavy chain: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
A

C
B

D
H

E
L

Spike protein

Human polyclonal Fab model with polyalanine backbone - Heavy chain

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